Boris Johnson was accused of betraying UK fishermen yesterday by handing lucrative licences to foreign firms, including New Zealand company Sanford.
The row erupted after it emerged that £75 million ($145m) worth of licences in the South Atlantic have been handed to firms from Norway, Chile and New Zealand.
Applications from two British-based companies – South Georgia Fisheries and Fortuna Ltd – were rejected, according to the Daily Mail.
The decision has angered the firms which operate in the Falkland Islands and critics say it makes a mockery of the Foreign Secretary's pledge to take back control of British waters by leaving the EU.
Six licences allowing access to 200 square miles around the British overseas territory of South Georgia for four years were granted in February.
Four went to vessels from the Norwegian firm Ervik Havfiske, of which three are believed to be sailing under the flag of the British overseas territory of St Helena for Argos Frayanes Ltd, a subsidiary of Ervik Havfiske.
One went to a New Zealand ship called San Aspiring - a 51.2m vessel owned and operated by Sanford - and the final one to Chile's Antarctic Bay.
Although the decisions were made by the government of South Georgia and South Sandwich Islands, which shares some administrative functions with the Falklands, they were based on advice from the Foreign Office.
Last night one of the failed bidders revealed he had launched a judicial review into the decision.
Rupert Street, chief executive of South Georgia Fisheries, said: "This betrayal of British fishermen makes clear the hollow promises of the Government when it comes to control of our waters.
"When the Government had the opportunity to give UK fishermen the chance to fish our own waters again, Boris Johnson has instead given the prize to our foreign competitors seemingly to boost the Government's foreign policy rather than to help British business or even just on the merits of the case.
"I fear for colleagues in the North Sea and for what they can expect post-Brexit if this murky deal with the Norwegians is anything to go by."
James Wallace, from Fortuna, said Britain had "sold out the Falklands". He accused ministers of "waving the flag" to foster relationships with non-EU member states while rejecting the bids of British vessels and "giving four four-year licenses to vessels owned in Norway".
Johnson has repeatedly promised that Brexit will lead to Britain taking back control.
But Street said the decision made on South Georgian fishing rights indicated otherwise. He has now filed for a judicial review through the High Court of the Falkland Islands and the case will be passed on to a British judge.
Tensions over post-Brexit fishing rights were highlighted last month when former Ukip leader Nigel Farage joined protesters opposed to the transition deal being negotiated with the EU dumped fish into the Thames.
Street said: "If we don't have a government that supports fisheries, how can we do anything post-Brexit?"
His firm is a Falkland Islands company paying Falkland Islands corporation tax, with a UK majority shareholder paying UK tax. The other company that lost out is Fortuna. It was the first locally owned firm to fish in Falklands waters shortly after the declaration of the islands' conservation zones in 1987.
A judge will now decide whether Street's firm has legitimate grounds for the case.
Teslyn Barkman, a member of the Falkland Islands Legislative Assembly, said: 'Why does the (South Georgia Fisheries) application process allow a foreign policy ambition to go against an overseas territory's prosperity?'
It is understood the Foreign Office ordered that one licence was set aside for a Chilean-registered boat.
Last night a spokesman for the department admitted it took into account the foreign policy benefits of allocating licences to regional partners.
However, she added: "The recent licensing round resulted in three of six licenses being awarded to British vessels: each flagged to the UK overseas territory St Helena, chartered and operated by a British company.
"The fact that a vessel is built in Norway, or whether company chooses to operate commercially with Norwegian partners, is not among the primary considerations for licensing."